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- EMDB-61622: Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in ... -

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Entry
Database: EMDB / ID: EMD-61622
TitleStructure of native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus
Map data
Sample
  • Tissue: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus
    • Complex: NMDA receptor
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Complex: Fab
      • Complex: Fab 4F11
        • Protein or peptide: Heavy Chain of GluN1 Fab, 4F11
        • Protein or peptide: Light Chain of GluN1 Fab, 4F11
      • Complex: Fab2
        • Protein or peptide: Heavy Chain of GluN2B Fab2
        • Protein or peptide: Light Chain of GluN2B Fab2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
KeywordsMEMBRANE PROTEIN / native NMDA receptor / adult rat cartex & hippocampus / GluN2A / GluN2B / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / response to hydrogen sulfide / regulation of respiratory gaseous exchange / response to other organism / positive regulation of inhibitory postsynaptic potential / protein localization to postsynaptic membrane / apical dendrite / regulation of ARF protein signal transduction / response to methylmercury / fear response / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / response to carbohydrate / cellular response to dsRNA / interleukin-1 receptor binding / negative regulation of dendritic spine maintenance / cellular response to lipid / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / response to manganese ion / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / heterocyclic compound binding / glycine binding / positive regulation of reactive oxygen species biosynthetic process / receptor clustering / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / regulation of postsynaptic membrane potential / response to amine / small molecule binding / startle response / social behavior / monoatomic cation transmembrane transport / associative learning / : / behavioral response to pain / response to magnesium ion / regulation of MAPK cascade / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / behavioral fear response / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / synaptic cleft / prepulse inhibition / multicellular organismal response to stress / detection of mechanical stimulus involved in sensory perception of pain / phosphatase binding / response to electrical stimulus / monoatomic cation channel activity / glutamate-gated receptor activity / response to mechanical stimulus / calcium ion homeostasis / response to fungicide / D2 dopamine receptor binding / cell adhesion molecule binding / ionotropic glutamate receptor binding
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsZhang M / Feng J / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell / Year: 2025
Title: Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus.
Authors: Ming Zhang / Juan Feng / Chun Xie / Nan Song / Chaozhi Jin / Jian Wang / Qun Zhao / Lihua Zhang / Boshuang Wang / Yidi Sun / Fei Guo / Yang Li / Shujia Zhu /
Abstract: The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). ...The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). However, subunit assembly and molecular architecture of endogenous NMDARs (eNMDARs) in the brain remain elusive. Using conformation- and subunit-dependent antibodies, we purified eNMDARs from adult rat cerebral cortex and hippocampus. Three major subtypes of GluN1-N2A-N2B, GluN1-N2B, and GluN1-N2A eNMDARs were resolved by cryoelectron microscopy (cryo-EM) at the resolution up to 4.2 Å. The particle ratio of these three subtypes was 9:7:4, indicating that about half of GluN2A and GluN2B subunits are incorporated into the tri-heterotetramers. Structural analysis revealed the asymmetric architecture of the GluN1-N2A-N2B receptor throughout the extracellular to the transmembrane layers. Moreover, the conformational variations between GluN1-N2B and GluN1-N2A-N2B receptors revealed the distinct biophysical properties across different eNMDAR subtypes. Our findings imply the structural and functional complexity of eNMDARs and shed light on structure-based therapeutic design targeting these eNMDARs in vivo.
History
DepositionSep 23, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61622.png

Downloads & links

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Map

FileDownload / File: emd_61622.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.72 Å		1.07 Å/pix.
x 320 pix.
= 342.72 Å		1.07 Å/pix.
x 320 pix.
= 342.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.052
Minimum - Maximum-0.2295606 - 0.36516988
Average (Standard dev.)0.0010037747 (±0.013296957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61622_msk_1.map
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Half map: #2

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Half map: #1

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Sample components

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Entire : Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex an...

EntireName: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus
Components
  • Tissue: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus
    • Complex: NMDA receptor
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
      • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Complex: Fab
      • Complex: Fab 4F11
        • Protein or peptide: Heavy Chain of GluN1 Fab, 4F11
        • Protein or peptide: Light Chain of GluN1 Fab, 4F11
      • Complex: Fab2
        • Protein or peptide: Heavy Chain of GluN2B Fab2
        • Protein or peptide: Light Chain of GluN2B Fab2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

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Supramolecule #1: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex an...

SupramoleculeName: Native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: NMDA receptor

SupramoleculeName: NMDA receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Fab 4F11

SupramoleculeName: Fab 4F11 / type: complex / ID: 3 / Parent: 5 / Macromolecule list: #3-#4

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Supramolecule #4: Fab2

SupramoleculeName: Fab2 / type: complex / ID: 4 / Parent: 5 / Macromolecule list: #5-#6

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Supramolecule #5: Fab

SupramoleculeName: Fab / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 91.996172 KDa
SequenceString: KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLNATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE ...String:
KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLNATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE KVLQFDPGTK NVTALLMEAR ELEARVIILS ASEDDAATVY RAAAMLNMTG SGYVWLVGER EISGNALRYA PD GIIGLQL INGKNESAHI SDAVGVVAQA VHELLEKENI TDPPRGCVGN TNIWKTGPLF KRVLMSSKYA DGVTGRVEFN EDG DRKFAN YSIMNLQNRK LVQVGIYNGT HVIPNDRKII WPGGETEKPR GYQMSTRLKI VTIHQEPFVY VKPTMSDGTC KEEF TVNGD PVKKVICTGP NDTSPGSPRH TVPQCCYGFC IDLLIKLART MNFTYEVHLV ADGKFGTQER VNNSNKKEWN GMMGE LLSG QADMIVAPLT INNERAQYIE FSKPFKYQGL TILVKKEIPR STLDSFMQPF QSTLWLLVGL SVHVVAVMLY LLDRFS PFG RFKVNSEEEE EDALTLSSAM WFSWGVLLNS GIGEGAPRSF SARILGMVWA GFAMIIVASY TANLAAFLVL DRPEERI TG INDPRLRNPS DKFIYATVKQ SSVDIYFRRQ VELSTMYRHM EKHNYESAAE AIQAVRDNKL HAFIWDSAVL EFEASQKC D LVTTGELFFR SGFGIGMRKD SPWKQNVSLS ILKSHENGFM EDLDKTWVRY QECDSRSNAP ATLTFENMAG VFMLVAGGI VAGIFLIFIE IAYKRHK

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 91.182109 KDa
SequenceString: IGIAVILVGT SDEVAIKDAH EKDDFHHLSV VPRVELVAMN ETDPKSIITR ICDLMSDRKI QGVVFADDTD QEAIAQILDF ISAQTLTPI LGIHGGSSMI MADKDESSMF FQFGPSIEQQ ASVMLNIMEE YDWYIFSIVT TYFPGYQDFV NKIRSTIENS F VGWELEEV ...String:
IGIAVILVGT SDEVAIKDAH EKDDFHHLSV VPRVELVAMN ETDPKSIITR ICDLMSDRKI QGVVFADDTD QEAIAQILDF ISAQTLTPI LGIHGGSSMI MADKDESSMF FQFGPSIEQQ ASVMLNIMEE YDWYIFSIVT TYFPGYQDFV NKIRSTIENS F VGWELEEV LLLDMSLDDG DSKIQNQLKK LQSPIILLYC TKEEATYIFE VANSVGLTGY GYTWIVPSLV AGDTDTVPSE FP TGLISVS YDEWDYGLPA RVRDGIAIIT TAASDMLSEH SFIPEPKSSC YNTHEKRIYQ SNMLNRYLIN VTFEGRNLSF SED GYQMHP KLVIILLNKE RKWERVGKWK DKSLQMKYYV WPRMCPETEE QEDDHLSIVT LEEAPFVIVE SVDPLSGTCM RNTV PCQKR IISENKTDEE PGYIKKCCKG FCIDILKKIS KSVKFTYDLY LVTNGKHGKK INGTWNGMIG EVVMKRAYMA VGSLT INEE RSEVVDFSVP FIETGISVMV SRSNGTVSPS AFLEPFSADV WVMMFVMLLI VSAVAVFVFE YFSPVGYNRC LADGRE PGG PSFTIGKAIW LLWGLVFNNS VPVQNPKGTT SKIMVSVWAF FAVIFLASYT ANLAAFMIQE EYVDQVSGLS DKKFQRP ND FSPPFRFGTV PNGSTERNIR NNYAEMHAYM GKFNQRGVDD ALLSLKTGKL DAFIYDAAVL NYMAGRDEGC KLVTIGSG K VFASTGYGIA IQKDSGWKRQ VDLAILQLFG DGEMEELEAL WLTGICHNEK NEVMSSQLDI DNMAGVFYML GAAMALSLI TFICEHLFYW Q

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: Heavy Chain of GluN1 Fab, 4F11

MacromoleculeName: Heavy Chain of GluN1 Fab, 4F11 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.306682 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNKLEWMG YISYSGSTGY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARL YYGFYGMDYW GQGTSVTVS

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Macromolecule #4: Light Chain of GluN1 Fab, 4F11

MacromoleculeName: Light Chain of GluN1 Fab, 4F11 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.78395 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
IVLTQSPASL AVSLGQRATI SCKASQSVDY DGNSYMNWYQ QKPGQPPKLL IYAASNLESG IPARFSGSGS GTDFTLNIHP VEEEDAATY YCQQGNEDPP TFGGGTKLEI K

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Macromolecule #5: Heavy Chain of GluN2B Fab2

MacromoleculeName: Heavy Chain of GluN2B Fab2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.994521 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
VKLQESGGGL VQPGGSLKLS CAASGFTFSS YTMSWVRQTP EKRLEWVAYI SNGGGGTYYP DTVKGRFTIS RDNAKNTLYL QMNSLKEDT AMYYCARPSR GGSSYWYFDV WGAGTTVTV

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Macromolecule #6: Light Chain of GluN2B Fab2

MacromoleculeName: Light Chain of GluN2B Fab2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.659048 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
DIQMTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSSLQPGIPS RFSGSGSGRD YSFSISNLEP EDIATYYCL QYDNLYTFGG GTKLEIK

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 14 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #10: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

MacromoleculeName: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
type: ligand / ID: 10 / Number of copies: 2 / Formula: 7RC
Molecular weightTheoretical: 252.205 Da
Chemical component information

ChemComp-7RC:
(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36786
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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